Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10198/24219 |
Resumo: | Pollen metabarcoding is emerging as a powerful tool for ecological research and offers unprecedented scale in citizen science projects for environmental monitoring via honey bees. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is at the forefront of the pipeline. While in metabarcoding studies pollen has been preserved at − 20 °C (FRZ), this is not the best method for citizen scientists. Herein, we compared this method with ethanol (EtOH), silica gel (SG) and room temperature (RT) for preservation of pollen collected from hives in Austria and Denmark. After ~ 4 months of storage, DNAs were extracted with a food kit, and their quality and concentration measured. Most DNA extracts exhibited 260/280 absorbance ratios close to the optimal 1.8, with RT samples from Austria performing slightly worse than FRZ and SG samples (P < 0.027). Statistical differences were also detected for DNA concentration, with EtOH samples producing lower yields than RT and FRZ samples in both countries and SG in Austria (P < 0.042). Yet, qualitative and quantitative assessments of floral composition obtained using high-throughput sequencing with the ITS2 barcode gave non-significant effects of preservation methods on richness, relative abundance and Shannon diversity, in both countries. While freezing and ethanol are commonly employed for archiving tissue for molecular applications, desiccation is cheaper and easier to use regarding both storage and transportation. Since SG is less dependent on ambient humidity and less prone to contamination than RT, we recommend SG for preserving pollen for metabarcoding. SG is straightforward for laymen to use and hence robust for widespread application in citizen science studies. |
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Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcodingDNA metabarcodingPollenDNA barcodingPreservation biasSilica gelPreservationCitizen sciencePollen metabarcoding is emerging as a powerful tool for ecological research and offers unprecedented scale in citizen science projects for environmental monitoring via honey bees. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is at the forefront of the pipeline. While in metabarcoding studies pollen has been preserved at − 20 °C (FRZ), this is not the best method for citizen scientists. Herein, we compared this method with ethanol (EtOH), silica gel (SG) and room temperature (RT) for preservation of pollen collected from hives in Austria and Denmark. After ~ 4 months of storage, DNAs were extracted with a food kit, and their quality and concentration measured. Most DNA extracts exhibited 260/280 absorbance ratios close to the optimal 1.8, with RT samples from Austria performing slightly worse than FRZ and SG samples (P < 0.027). Statistical differences were also detected for DNA concentration, with EtOH samples producing lower yields than RT and FRZ samples in both countries and SG in Austria (P < 0.042). Yet, qualitative and quantitative assessments of floral composition obtained using high-throughput sequencing with the ITS2 barcode gave non-significant effects of preservation methods on richness, relative abundance and Shannon diversity, in both countries. While freezing and ethanol are commonly employed for archiving tissue for molecular applications, desiccation is cheaper and easier to use regarding both storage and transportation. Since SG is less dependent on ambient humidity and less prone to contamination than RT, we recommend SG for preserving pollen for metabarcoding. SG is straightforward for laymen to use and hence robust for widespread application in citizen science studies.We are deeply indebted to Susana Lopes and Maria Magalhães, from CIBIO—Research Centre in Biodiversity and Genetic Resources—InBIO Associate Laboratory, for their time devoted to library preparation and sequencing in the MiSeq. AQ acknowledges the PhD scholarship (DFA/BD/5155/2020) funded by FCT. This work was funded by the Health and Food Safety Directorate General, European Commission through the project INSIGNIA—Environmental monitoring of pesticide use through honeybees SANTE/E4/SI2.788418-SI2.788452- INSIGINIA-PP-1–1-2018. Fundação para a Ciência e a Tecnologia (FCT) provided financial support by national funds (FCT/MCTES) to CIMO (UIDB/00690/2020).Biblioteca Digital do IPBQuaresma, AndreiaBrodschneider, RobertGratzer, KristinaGray, AlisonKeller, AlexanderKilpinen, OleRufino, JoséSteen, Jozef van derVejsnæs, FlemmingPinto, M. Alice2021-11-17T15:53:01Z20212021-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10198/24219engQuaresma, Andreia; Brodschneider, Robert; Gratzer, Kristina; Gray, Alison; Keller, Alexander; Kilpinen, Ole; Rufino, José; Steen, Jozef van der; Vejsnæs, Flemming; Pinto, M. Alice (2021). Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding. Environmental Monitoring and Assessment. ISSN 0167-6369. 193:12, p. 1-200167-636910.1007/s10661-021-09563-4info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-21T10:54:07Zoai:bibliotecadigital.ipb.pt:10198/24219Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T23:15:04.141973Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding |
title |
Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding |
spellingShingle |
Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding Quaresma, Andreia DNA metabarcoding Pollen DNA barcoding Preservation bias Silica gel Preservation Citizen science |
title_short |
Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding |
title_full |
Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding |
title_fullStr |
Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding |
title_full_unstemmed |
Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding |
title_sort |
Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding |
author |
Quaresma, Andreia |
author_facet |
Quaresma, Andreia Brodschneider, Robert Gratzer, Kristina Gray, Alison Keller, Alexander Kilpinen, Ole Rufino, José Steen, Jozef van der Vejsnæs, Flemming Pinto, M. Alice |
author_role |
author |
author2 |
Brodschneider, Robert Gratzer, Kristina Gray, Alison Keller, Alexander Kilpinen, Ole Rufino, José Steen, Jozef van der Vejsnæs, Flemming Pinto, M. Alice |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Biblioteca Digital do IPB |
dc.contributor.author.fl_str_mv |
Quaresma, Andreia Brodschneider, Robert Gratzer, Kristina Gray, Alison Keller, Alexander Kilpinen, Ole Rufino, José Steen, Jozef van der Vejsnæs, Flemming Pinto, M. Alice |
dc.subject.por.fl_str_mv |
DNA metabarcoding Pollen DNA barcoding Preservation bias Silica gel Preservation Citizen science |
topic |
DNA metabarcoding Pollen DNA barcoding Preservation bias Silica gel Preservation Citizen science |
description |
Pollen metabarcoding is emerging as a powerful tool for ecological research and offers unprecedented scale in citizen science projects for environmental monitoring via honey bees. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is at the forefront of the pipeline. While in metabarcoding studies pollen has been preserved at − 20 °C (FRZ), this is not the best method for citizen scientists. Herein, we compared this method with ethanol (EtOH), silica gel (SG) and room temperature (RT) for preservation of pollen collected from hives in Austria and Denmark. After ~ 4 months of storage, DNAs were extracted with a food kit, and their quality and concentration measured. Most DNA extracts exhibited 260/280 absorbance ratios close to the optimal 1.8, with RT samples from Austria performing slightly worse than FRZ and SG samples (P < 0.027). Statistical differences were also detected for DNA concentration, with EtOH samples producing lower yields than RT and FRZ samples in both countries and SG in Austria (P < 0.042). Yet, qualitative and quantitative assessments of floral composition obtained using high-throughput sequencing with the ITS2 barcode gave non-significant effects of preservation methods on richness, relative abundance and Shannon diversity, in both countries. While freezing and ethanol are commonly employed for archiving tissue for molecular applications, desiccation is cheaper and easier to use regarding both storage and transportation. Since SG is less dependent on ambient humidity and less prone to contamination than RT, we recommend SG for preserving pollen for metabarcoding. SG is straightforward for laymen to use and hence robust for widespread application in citizen science studies. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-11-17T15:53:01Z 2021 2021-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10198/24219 |
url |
http://hdl.handle.net/10198/24219 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Quaresma, Andreia; Brodschneider, Robert; Gratzer, Kristina; Gray, Alison; Keller, Alexander; Kilpinen, Ole; Rufino, José; Steen, Jozef van der; Vejsnæs, Flemming; Pinto, M. Alice (2021). Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding. Environmental Monitoring and Assessment. ISSN 0167-6369. 193:12, p. 1-20 0167-6369 10.1007/s10661-021-09563-4 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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